VIRMA
protein-codingvir like m6A methyltransferase associated, the group of Armadillo like helical domain containing|m6A methyltransferase complex|WTAP complex
Gene summary
Enables RNA binding activity. Involved in mRNA processing. Located in RNA N6-methyladenosine methyltransferase complex and nuclear speck. [provided by Alliance of Genome Resources, Jun 2026]
- KIAA1429
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~65.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to VIRMA variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015496.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 169 | 4 | 173 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 177 | 4 | 0 | 181 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056311.2 | 24 | MANE Select | |
| Ensembl | ENSP00000297591.5 | 24 | MANE Select | |
| RefSeq | NP_892121.1 | 13 | Standard | |
| Ensembl | ENSP00000398390.2 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- mRNA processing
- multicellular organism development
- RNA splicing
- mRNA methylation
- mRNA alternative polyadenylation
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleoplasm
- cytosol
- nuclear body
- nuclear speck
- RNA N6-methyladenosine methyltransferase complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000297591
- Coding exons
- 24
- Length
- 65837
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 39
- Defined
- 125748
- p
- 0.000155
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.77 | 706 | 946 | 0.746 | 0.0000480 | 11827 |
| Missense (PolyPhen) | 224 | 402.26 | 0.55686 | 4905 | ||
| Synonymous | -0.313 | 335 | 328 | 1.02 | 0.0000157 | 3522 |
| Loss of Function | 6.83 | 15 | 81.5 | 0.184 | 0.00000448 | 1043 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0.00022 | 0.00020 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00021 | 0.00019 | rare |
| South Asian | 0.00013 | 0.000098 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that plays a role in the efficiency of mRNA splicing and RNA processing (PubMed:24981863, PubMed:29507755). Acts as a key regulator of m6A methylation by promoting m6A methylation of mRNAs in the 3'-UTR near the stop codon: recruits the catalytic core components METTL3 and METTL14, thereby guiding m6A methylation at specific sites (PubMed:29507755). Required for mRNA polyadenylation via its role in selective m6A methylation: m6A methylation of mRNAs in the 3'-UTR near the stop codon correlating with alternative polyadenylation (APA) (PubMed:29507755). {ECO:0000269|PubMed:24981863, ECO:0000269|PubMed:29507755}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- RVIS EVS
- -1.37
- RVIS percentile EVS
- 4.52
Essentials
- Essential (gene trap)
- H